1 | """ |
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2 | This module provide GUI for the neutron scattering length density calculator |
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3 | |
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4 | """ |
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5 | |
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6 | import wx |
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7 | import math |
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8 | import sys |
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9 | |
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10 | from sans.guiframe.panel_base import PanelBase |
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11 | |
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12 | from sans.guiframe.utils import format_number |
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13 | from sans.guiframe.utils import check_float |
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14 | from sans.guiframe.events import StatusEvent |
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15 | |
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16 | # the calculator default value for wavelength is 6 |
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17 | #import periodictable |
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18 | from periodictable import formula |
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19 | from periodictable.xsf import xray_energy |
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20 | from periodictable.xsf import xray_sld_from_atoms |
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21 | from periodictable.nsf import neutron_scattering |
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22 | |
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23 | WAVELENGTH = 6.0 |
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24 | _BOX_WIDTH = 76 |
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25 | _STATICBOX_WIDTH = 350 |
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26 | _SCALE = 1e-6 |
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27 | |
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28 | #SLD panel size |
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29 | if sys.platform.count("win32") > 0: |
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30 | _STATICBOX_WIDTH = 350 |
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31 | PANEL_SIZE = 400 |
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32 | FONT_VARIANT = 0 |
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33 | else: |
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34 | _STATICBOX_WIDTH = 380 |
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35 | PANEL_SIZE = 410 |
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36 | FONT_VARIANT = 1 |
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37 | |
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38 | class SldPanel(wx.Panel, PanelBase): |
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39 | """ |
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40 | Provides the SLD calculator GUI. |
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41 | """ |
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42 | ## Internal nickname for the window, used by the AUI manager |
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43 | window_name = "SLD Calculator" |
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44 | ## Name to appear on the window title bar |
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45 | window_caption = "SLD Calculator" |
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46 | ## Flag to tell the AUI manager to put this panel in the center pane |
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47 | CENTER_PANE = True |
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48 | |
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49 | def __init__(self, parent, base=None, *args, **kwds): |
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50 | """ |
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51 | """ |
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52 | wx.Panel.__init__(self, parent, *args, **kwds) |
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53 | PanelBase.__init__(self) |
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54 | #Font size |
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55 | self.SetWindowVariant(variant=FONT_VARIANT) |
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56 | # Object that receive status event |
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57 | self.base = base |
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58 | self.wavelength = WAVELENGTH |
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59 | #layout attribute |
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60 | self.compound_ctl = None |
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61 | self.density_ctl = None |
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62 | self.compound = "" |
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63 | self.density = "" |
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64 | self.wavelength_ctl = None |
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65 | self.neutron_sld_real_ctl = None |
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66 | self.neutron_sld_im_ctl = None |
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67 | self.mo_ka_sld_real_ctl = None |
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68 | self.mo_ka_sld_im_ctl = None |
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69 | self.cu_ka_sld_real_ctl = None |
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70 | self.cu_ka_sld_im_ctl = None |
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71 | self.neutron_abs_ctl = None |
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72 | self.neutron_inc_ctl = None |
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73 | self.neutron_length_ctl = None |
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74 | self.button_calculate = None |
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75 | #Draw the panel |
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76 | self._do_layout() |
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77 | self.SetAutoLayout(True) |
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78 | self.Layout() |
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79 | |
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80 | def _do_layout(self): |
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81 | """ |
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82 | Draw window content |
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83 | """ |
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84 | unit_a = '[A]' |
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85 | unit_density = '[g/cm^(3)]' |
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86 | unit_sld = '[1/A^(2)]' |
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87 | unit_cm1 = '[1/cm]' |
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88 | unit_cm = '[cm]' |
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89 | sizer_input = wx.GridBagSizer(5, 5) |
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90 | sizer_output = wx.GridBagSizer(5, 5) |
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91 | sizer_button = wx.BoxSizer(wx.HORIZONTAL) |
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92 | sizer1 = wx.BoxSizer(wx.HORIZONTAL) |
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93 | sizer2 = wx.BoxSizer(wx.HORIZONTAL) |
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94 | sizer3 = wx.BoxSizer(wx.HORIZONTAL) |
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95 | #---------inputs---------------- |
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96 | inputbox = wx.StaticBox(self, -1, "Input") |
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97 | boxsizer1 = wx.StaticBoxSizer(inputbox, wx.VERTICAL) |
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98 | boxsizer1.SetMinSize((_STATICBOX_WIDTH, -1)) |
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99 | |
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100 | compound_txt = wx.StaticText(self, -1, 'Compound ') |
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101 | self.compound_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH*2, -1)) |
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102 | density_txt = wx.StaticText(self, -1, 'Density ') |
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103 | self.density_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH, -1)) |
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104 | unit_density_txt = wx.StaticText(self, -1, unit_density) |
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105 | wavelength_txt = wx.StaticText(self, -1, 'Wavelength ') |
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106 | self.wavelength_ctl = wx.TextCtrl(self, -1, size=(_BOX_WIDTH, -1)) |
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107 | self.wavelength_ctl.SetValue(str(self.wavelength)) |
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108 | unit_a_txt = wx.StaticText(self, -1, unit_a) |
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109 | iy = 0 |
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110 | ix = 0 |
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111 | sizer_input.Add(compound_txt, (iy, ix), (1, 1), |
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112 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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113 | ix += 1 |
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114 | sizer_input.Add(self.compound_ctl, (iy, ix), (1, 1), |
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115 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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116 | iy += 1 |
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117 | ix = 0 |
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118 | sizer_input.Add(density_txt, (iy, ix), (1, 1), |
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119 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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120 | ix += 1 |
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121 | sizer_input.Add(self.density_ctl, (iy, ix), (1, 1), |
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122 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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123 | ix +=1 |
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124 | sizer_input.Add(unit_density_txt,(iy, ix), (1, 1), |
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125 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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126 | iy += 1 |
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127 | ix = 0 |
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128 | sizer_input.Add(wavelength_txt, (iy, ix), (1, 1), |
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129 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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130 | ix += 1 |
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131 | sizer_input.Add(self.wavelength_ctl, (iy, ix), (1, 1), |
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132 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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133 | ix += 1 |
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134 | sizer_input.Add(unit_a_txt, (iy, ix), (1, 1), |
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135 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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136 | boxsizer1.Add(sizer_input) |
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137 | sizer1.Add(boxsizer1, 0, wx.EXPAND | wx.ALL, 10) |
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138 | #---------Outputs sizer-------- |
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139 | outputbox = wx.StaticBox(self, -1, "Output") |
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140 | boxsizer2 = wx.StaticBoxSizer(outputbox, wx.VERTICAL) |
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141 | boxsizer2.SetMinSize((_STATICBOX_WIDTH, -1)) |
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142 | |
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143 | i_complex = '- i' |
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144 | neutron_sld_txt = wx.StaticText(self, -1, 'Neutron SLD') |
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145 | self.neutron_sld_real_ctl = wx.TextCtrl(self, -1, |
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146 | size=(_BOX_WIDTH, -1)) |
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147 | self.neutron_sld_real_ctl.SetEditable(False) |
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148 | self.neutron_sld_real_ctl.SetToolTipString("Neutron SLD real.") |
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149 | self.neutron_sld_im_ctl = wx.TextCtrl(self, -1, |
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150 | size=(_BOX_WIDTH, -1)) |
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151 | self.neutron_sld_im_ctl.SetEditable(False) |
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152 | self.neutron_sld_im_ctl.SetToolTipString("Neutron SLD imaginary.") |
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153 | neutron_sld_units_txt = wx.StaticText(self, -1, unit_sld) |
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154 | |
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155 | cu_ka_sld_txt = wx.StaticText(self, -1, 'Cu Ka SLD') |
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156 | self.cu_ka_sld_real_ctl = wx.TextCtrl(self, -1, |
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157 | size=(_BOX_WIDTH, -1)) |
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158 | self.cu_ka_sld_real_ctl.SetEditable(False) |
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159 | self.cu_ka_sld_real_ctl.SetToolTipString("Cu Ka SLD real.") |
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160 | self.cu_ka_sld_im_ctl = wx.TextCtrl(self, -1, |
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161 | size=(_BOX_WIDTH, -1)) |
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162 | self.cu_ka_sld_im_ctl.SetEditable(False) |
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163 | self.cu_ka_sld_im_ctl.SetToolTipString("Cu Ka SLD imaginary.") |
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164 | cu_ka_sld_units_txt = wx.StaticText(self, -1, unit_sld) |
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165 | |
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166 | mo_ka_sld_txt = wx.StaticText(self, -1, 'Mo Ka SLD') |
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167 | self.mo_ka_sld_real_ctl = wx.TextCtrl(self, -1, |
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168 | size=(_BOX_WIDTH, -1)) |
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169 | self.mo_ka_sld_real_ctl.SetEditable(False) |
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170 | self.mo_ka_sld_real_ctl.SetToolTipString("Mo Ka SLD real.") |
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171 | self.mo_ka_sld_im_ctl = wx.TextCtrl(self, -1, |
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172 | size=(_BOX_WIDTH, -1)) |
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173 | self.mo_ka_sld_im_ctl.SetEditable(False) |
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174 | self.mo_ka_sld_im_ctl.SetToolTipString("Mo Ka SLD imaginary.") |
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175 | mo_ka_sld_units_txt = wx.StaticText(self, -1, unit_sld) |
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176 | |
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177 | neutron_inc_txt = wx.StaticText(self, -1, 'Neutron Inc. Xs') |
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178 | self.neutron_inc_ctl = wx.TextCtrl(self, -1, |
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179 | size=(_BOX_WIDTH, -1)) |
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180 | self.neutron_inc_ctl.SetEditable(False) |
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181 | self.neutron_inc_ctl.SetToolTipString("Neutron Inc. Xs") |
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182 | neutron_inc_units_txt = wx.StaticText(self, -1, unit_cm1) |
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183 | |
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184 | neutron_abs_txt = wx.StaticText(self, -1, 'Neutron Abs. Xs') |
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185 | self.neutron_abs_ctl = wx.TextCtrl(self, -1, |
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186 | size=(_BOX_WIDTH, -1)) |
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187 | self.neutron_abs_ctl.SetEditable(False) |
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188 | self.neutron_abs_ctl.SetToolTipString("Neutron Abs. Xs") |
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189 | neutron_abs_units_txt = wx.StaticText(self, -1, unit_cm1) |
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190 | |
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191 | neutron_length_txt = wx.StaticText(self, -1, 'Neutron 1/e length') |
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192 | self.neutron_length_ctl = wx.TextCtrl(self, -1, |
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193 | size=(_BOX_WIDTH, -1)) |
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194 | self.neutron_length_ctl.SetEditable(False) |
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195 | self.neutron_length_ctl.SetToolTipString("Neutron 1/e length") |
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196 | neutron_length_units_txt = wx.StaticText(self, -1, unit_cm) |
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197 | |
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198 | iy = 0 |
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199 | ix = 0 |
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200 | sizer_output.Add(neutron_sld_txt, (iy, ix), (1, 1), |
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201 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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202 | ix += 1 |
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203 | sizer_output.Add(self.neutron_sld_real_ctl, (iy, ix), (1, 1), |
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204 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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205 | ix += 1 |
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206 | sizer_output.Add(wx.StaticText(self, -1, i_complex), |
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207 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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208 | ix += 1 |
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209 | sizer_output.Add(self.neutron_sld_im_ctl, |
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210 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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211 | ix += 1 |
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212 | sizer_output.Add(neutron_sld_units_txt, |
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213 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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214 | iy += 1 |
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215 | ix = 0 |
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216 | sizer_output.Add(cu_ka_sld_txt, (iy, ix), (1, 1), |
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217 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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218 | ix += 1 |
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219 | sizer_output.Add(self.cu_ka_sld_real_ctl, (iy, ix), (1, 1), |
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220 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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221 | ix += 1 |
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222 | sizer_output.Add(wx.StaticText(self, -1, i_complex), |
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223 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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224 | ix += 1 |
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225 | sizer_output.Add(self.cu_ka_sld_im_ctl, |
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226 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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227 | ix += 1 |
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228 | sizer_output.Add(cu_ka_sld_units_txt, |
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229 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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230 | iy += 1 |
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231 | ix = 0 |
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232 | sizer_output.Add(mo_ka_sld_txt,(iy, ix), (1, 1), |
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233 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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234 | ix += 1 |
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235 | sizer_output.Add(self.mo_ka_sld_real_ctl,(iy, ix), (1, 1), |
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236 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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237 | ix += 1 |
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238 | sizer_output.Add(wx.StaticText(self, -1, i_complex), |
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239 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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240 | ix += 1 |
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241 | sizer_output.Add(self.mo_ka_sld_im_ctl, |
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242 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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243 | ix += 1 |
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244 | sizer_output.Add(mo_ka_sld_units_txt, |
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245 | (iy, ix), (1, 1), wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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246 | iy += 1 |
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247 | ix = 0 |
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248 | sizer_output.Add(neutron_inc_txt, (iy, ix), (1, 1), |
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249 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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250 | ix += 1 |
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251 | sizer_output.Add(self.neutron_inc_ctl, (iy, ix), (1, 1), |
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252 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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253 | ix += 2 |
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254 | sizer_output.Add(neutron_inc_units_txt,(iy, ix), (1, 1), |
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255 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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256 | iy += 1 |
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257 | ix = 0 |
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258 | sizer_output.Add(neutron_abs_txt, (iy, ix), (1, 1), |
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259 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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260 | ix += 1 |
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261 | sizer_output.Add(self.neutron_abs_ctl, (iy, ix), (1, 1), |
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262 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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263 | ix += 2 |
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264 | sizer_output.Add(neutron_abs_units_txt, (iy, ix), (1, 1), |
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265 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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266 | iy += 1 |
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267 | ix = 0 |
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268 | sizer_output.Add(neutron_length_txt, (iy, ix), (1, 1), |
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269 | wx.LEFT|wx.EXPAND|wx.ADJUST_MINSIZE, 15) |
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270 | ix += 1 |
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271 | sizer_output.Add(self.neutron_length_ctl, (iy, ix), (1, 1), |
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272 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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273 | ix += 2 |
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274 | sizer_output.Add(neutron_length_units_txt, (iy, ix), (1, 1), |
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275 | wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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276 | boxsizer2.Add(sizer_output) |
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277 | sizer2.Add(boxsizer2, 0, wx.EXPAND|wx.ALL, 10) |
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278 | #-----Button sizer------------ |
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279 | |
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280 | id = wx.NewId() |
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281 | self.button_calculate = wx.Button(self, id, "Calculate") |
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282 | self.button_calculate.SetToolTipString("Calculate SLD.") |
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283 | self.Bind(wx.EVT_BUTTON, self.calculateSld, id=id) |
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284 | |
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285 | sizer_button.Add((250, 20), 1, wx.EXPAND|wx.ADJUST_MINSIZE, 0) |
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286 | sizer_button.Add(self.button_calculate, 0, wx.RIGHT|wx.ADJUST_MINSIZE, 20) |
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287 | sizer3.Add(sizer_button) |
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288 | #---------layout---------------- |
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289 | vbox = wx.BoxSizer(wx.VERTICAL) |
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290 | vbox.Add(sizer1) |
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291 | vbox.Add(sizer2) |
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292 | vbox.Add(sizer3) |
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293 | vbox.Fit(self) |
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294 | self.SetSizer(vbox) |
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295 | |
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296 | def calculate_xray_sld(self, element): |
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297 | """ |
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298 | Get an element and compute the corresponding SLD for a given formula |
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299 | |
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300 | :param element: elements a string of existing atom |
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301 | |
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302 | """ |
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303 | myformula = formula(str(element)) |
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304 | if len(myformula.atoms) != 1: |
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305 | return |
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306 | element = myformula.atoms.keys()[0] |
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307 | energy = xray_energy(element.K_alpha) |
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308 | |
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309 | self.sld_formula = formula(str(self.compound), density=self.density) |
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310 | atom = self.sld_formula.atoms |
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311 | return xray_sld_from_atoms(atom, density=self.density, energy= energy) |
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312 | |
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313 | def check_inputs(self): |
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314 | """Check validity user inputs""" |
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315 | flag = True |
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316 | msg = "" |
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317 | if check_float(self.density_ctl): |
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318 | self.density = float(self.density_ctl.GetValue()) |
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319 | else: |
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320 | flag = False |
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321 | msg += "Error for Density value :expect float" |
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322 | |
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323 | self.wavelength = self.wavelength_ctl.GetValue() |
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324 | if str(self.wavelength).lstrip().rstrip() == "": |
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325 | self.wavelength = WAVELENGTH |
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326 | self.wavelength_ctl.SetValue(str(WAVELENGTH)) |
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327 | self.wavelength_ctl.SetBackgroundColour(wx.WHITE) |
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328 | self.wavelength_ctl.Refresh() |
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329 | msg += "Default value for wavelength is 6.0" |
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330 | else: |
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331 | if check_float(self.wavelength_ctl): |
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332 | self.wavelength = float(self.wavelength) |
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333 | else: |
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334 | flag = False |
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335 | msg += "Error for wavelength value :expect float" |
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336 | |
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337 | self.compound = self.compound_ctl.GetValue().lstrip().rstrip() |
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338 | if self.compound != "": |
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339 | try : |
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340 | formula(self.compound) |
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341 | self.compound_ctl.SetBackgroundColour(wx.WHITE) |
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342 | self.compound_ctl.Refresh() |
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343 | except: |
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344 | self.compound_ctl.SetBackgroundColour("pink") |
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345 | self.compound_ctl.Refresh() |
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346 | flag = False |
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347 | msg += "Enter correct formula" |
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348 | else: |
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349 | self.compound_ctl.SetBackgroundColour("pink") |
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350 | self.compound_ctl.Refresh() |
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351 | flag = False |
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352 | msg += "Enter a formula" |
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353 | return flag, msg |
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354 | |
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355 | def calculate_sld_helper(self, element, density, molecule_formula): |
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356 | """ |
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357 | Get an element and compute the corresponding SLD for a given formula |
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358 | |
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359 | :param element: elements a string of existing atom |
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360 | |
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361 | """ |
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362 | element_formula = formula(str(element)) |
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363 | if len(element_formula.atoms) != 1: |
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364 | return |
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365 | element = element_formula.atoms.keys()[0] |
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366 | energy = xray_energy(element.K_alpha) |
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367 | atom = molecule_formula.atoms |
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368 | return xray_sld_from_atoms(atom, density=density, energy=energy) |
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369 | |
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370 | |
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371 | def calculateSld(self, event): |
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372 | """ |
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373 | Calculate the neutron scattering density length of a molecule |
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374 | """ |
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375 | self.clear_outputs() |
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376 | try: |
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377 | #Check validity user inputs |
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378 | flag, msg = self.check_inputs() |
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379 | if self.base is not None and msg.lstrip().rstrip() != "": |
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380 | msg = "SLD Calculator: %s" % str(msg) |
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381 | wx.PostEvent(self.base, StatusEvent(status=msg)) |
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382 | if not flag: |
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383 | return |
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384 | #get ready to compute |
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385 | self.sld_formula = formula(self.compound, |
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386 | density=self.density) |
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387 | (sld_real, sld_im, _), (_, absorp, incoh), \ |
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388 | length = neutron_scattering(compound=self.compound, |
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389 | density=self.density, |
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390 | wavelength=self.wavelength) |
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391 | cu_real, cu_im = self.calculate_sld_helper(element="Cu", |
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392 | density=self.density, |
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393 | molecule_formula=self.sld_formula) |
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394 | mo_real, mo_im = self.calculate_sld_helper(element="Mo", |
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395 | density=self.density, |
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396 | molecule_formula=self.sld_formula) |
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397 | # set neutron sld values |
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398 | val = format_number(sld_real * _SCALE) |
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399 | self.neutron_sld_real_ctl.SetValue(val) |
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400 | val = format_number(math.fabs(sld_im) * _SCALE) |
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401 | self.neutron_sld_im_ctl.SetValue(val) |
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402 | # Compute the Cu SLD |
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403 | self.cu_ka_sld_real_ctl.SetValue(format_number(cu_real *_SCALE)) |
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404 | val = format_number(math.fabs(cu_im )* _SCALE) |
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405 | self.cu_ka_sld_im_ctl.SetValue(val) |
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406 | # Compute the Mo SLD |
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407 | self.mo_ka_sld_real_ctl.SetValue(format_number(mo_real *_SCALE)) |
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408 | val = format_number(math.fabs(mo_im)* _SCALE) |
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409 | self.mo_ka_sld_im_ctl.SetValue(val) |
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410 | # set incoherence and absorption |
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411 | self.neutron_inc_ctl.SetValue(format_number(incoh)) |
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412 | self.neutron_abs_ctl.SetValue(format_number(absorp)) |
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413 | # Neutron length |
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414 | self.neutron_length_ctl.SetValue(format_number(length)) |
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415 | # display wavelength |
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416 | self.wavelength_ctl.SetValue(str(self.wavelength)) |
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417 | except: |
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418 | if self.base is not None: |
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419 | msg = "SLD Calculator: %s"%(sys.exc_value) |
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420 | wx.PostEvent(self.base, StatusEvent(status=msg)) |
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421 | if event is not None: |
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422 | event.Skip() |
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423 | |
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424 | def clear_outputs(self): |
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425 | """ |
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426 | Clear the outputs textctrl |
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427 | """ |
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428 | self.neutron_sld_real_ctl.SetValue("") |
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429 | self.neutron_sld_im_ctl.SetValue("") |
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430 | self.mo_ka_sld_real_ctl.SetValue("") |
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431 | self.mo_ka_sld_im_ctl.SetValue("") |
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432 | self.cu_ka_sld_real_ctl.SetValue("") |
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433 | self.cu_ka_sld_im_ctl.SetValue("") |
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434 | self.neutron_abs_ctl.SetValue("") |
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435 | self.neutron_inc_ctl.SetValue("") |
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436 | self.neutron_length_ctl.SetValue("") |
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437 | |
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438 | |
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439 | class SldWindow(wx.Frame): |
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440 | """ |
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441 | """ |
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442 | def __init__(self, parent=None, title="SLD Calculator", |
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443 | base=None, size=(PANEL_SIZE, PANEL_SIZE), *args, **kwds): |
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444 | """ |
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445 | """ |
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446 | kwds['title'] = title |
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447 | kwds['size'] = size |
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448 | wx.Frame.__init__(self, parent, *args, **kwds) |
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449 | """ |
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450 | """ |
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451 | self.panel = SldPanel(self, base=base) |
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452 | self.Centre() |
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453 | self.Show(True) |
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454 | |
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455 | class ViewApp(wx.App): |
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456 | """ |
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457 | """ |
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458 | def OnInit(self): |
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459 | """ |
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460 | """ |
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461 | frame = SldWindow(None, title='SLD Calculator') |
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462 | frame.Show(True) |
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463 | self.SetTopWindow(frame) |
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464 | return True |
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465 | |
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466 | |
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467 | if __name__ == "__main__": |
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468 | app = ViewApp(0) |
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469 | app.MainLoop() |
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